How To Remove All Hypothetical Protein From Genbank File
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7.8 years ago
HG ★ 1.1k

Hi everyone after annotation one of sample genome i want to remove all hypothetical protein from genbank file. Can anyone give me any idea how to do simplest way ? Thank you advance.

genbank perl • 2.5k views
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It would help to see which part of the file (field) contains the annotation and an example.

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Do you need to keep the GenBank format? Maybe you can simply convert the GBK to Fasta and filter the sequences by description in the fasta comment line.

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7.1 years ago

You don't need BioPerl / BioPython for this. If you know how many lines your annotation takes up (assuming its fixed) - then you can do something like this from the command line in Linux

> sed 's/(\s{5}ANNOTATION_NAME\s+.+?\n)(.+?\n){NUMBEROFLINESTOREMOVE}//g' GENBANKFILE.gbk > NEWGENBANKFILE.gbk

Least - that's what worked for me when I ran into this issue.

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